Compiling modified Zacros executable

Some of the Zacros Wrapper functionality depends on additional output files which are not included in Zacros 1.02. Therefore, Zacros must be recompiled with modifications to the input files.

Installation instructions

  • Download the Zacros files from the Zacros website.
  • Replace the .f90 files in main folder with the ones in the Fortran_src folder from the Zacros-Wrapper repository.
  • Compile with cmake following the compiling instructions provided with Zacros. Using cmake ensures that the executable will run on the platform on which it is compiled.
  • Rename the executable file (.x in Unix, .exe in Windows) and put it in a directory that the Wrapper can access. You will need to provide a path to the executable when using the Zacros Wrapper.

Additional Zacros output files

Data in each file is in the form of a matrix of doubles. Each row corresponds to a time point. Time points are the same as in specnum_output.txt. Columns correspond to different elementary steps (first 3 files) or surface species (timeintspecs_output.txt).

File name Description
propensities_output.txt Instantaneous reaction propensities
timeintprop_output.txt Time integrated reaction propensities
trajderiv_output.txt Trajectory derivatives
timeintspecs_output.txt Time integrated surface species counts

Compiling on Farber

Farber <http://farber.hpc.udel.edu/> is a University of Delaware computing cluster. If you wish to compile Zacros on Farber you will need to make some configurational changes as the default compile settings are very inefficient.

  • Import the intel compiler: vpkg_require intel/2016
  • export CMAKE_Fortran_COMPILER=ifort
  • Usual installation
cd path/to/source/of/Zacros
mkdir build # If it does not exist yet
cd build
cmake .. -DCMAKE_BUILD_TYPE=Release
  • Instead of make as usual, type: ccmake .
  • Once within the ccmake, press t for advanced mode, then set the following flags
CMAKE_BUILD_TYPE=Release
OMP_NUM_PROCS=1
OpenMP_Fortran_FLAGS=-qopenmp
CMAKE_Fortran_COMPILER=ifort
  • Press c to configure, and then g to generate and exit. Finally: make